Ask for a tools which can mirror a result of FastaAlternateReferenceMaker to an annotation file
Hello. I have identified ~5000 genetic variants including SNPs, indels, and insertions in my yeast strain compared to s288c. Using FastaAlternateReferenceMaker, I made a new consensus sequence by incorporating all variants. Also, I want to change my annotation file as well because the indels and insertions changed the original genome position. Does GATK provide any tools such that I can change my annotation file corresponding to the generated consensus sequence?